Information Technology Reference
In-Depth Information
[19] Sali, A. and T.L. Blundell,
Definition of general topological equivalence in protein structures. A
procedure involving comparison of properties and relationships through simulated annealing and
dynamic programming.
J Mol Biol, 1990.
212
(2): p. 403-28.
[20] Sali, A., et al.,
From comparisons of protein sequences and structures to protein modelling and design.
Trends Biochem Sci, 1990.
15
(6): p. 235-40.
[21] Via, A., et al.,
Protein surface similarities: a survey of methods to describe and compare protein
surfaces.
Cell Mol Life Sci, 2000.
57
(13-14): p. 1970-7.
[22] Via, A., et al.,
Three-dimensional view of the surface motif associated with the P-loop structure: cis
and trans cases of convergent evolution.
J Mol Biol, 2000.
303
(4): p. 455-65.
[23] Pawlowski, K. and A. Godzik,
Surface map comparison: studying function diversity of homologous
proteins.
J Mol Biol, 2001.
309
(3): p. 793-806.
[24] Ankerst, M., et al.,
Nearest neighbor classification in 3D protein databases.
Proc Int Conf Intell Syst
Mol Biol, 1999: p. 34-43.
[25] Sneath, P.H. and R.R. Sokal,
Numerical Taxonomy
. 1973, San Fransisco: Freeman. 256.
[26] Kabsch, W.,
A solution for the best rotation to relate two sets of vectors.
Acta Crystallogr. A, 1976.
32
:
p. 922 -923.
[27] Carugo, O. and S. Pongor,
A normalized root-mean-square distance for comparing protein three-
dimensional structures.
Protein Sci, 2001.
10
(7): p. 1470-3.
[28] Johnson, M.S. and J.V. Lehtonen,
Comparison of protein three-dimensional structure
, in
Bioinformatics. Sequence, structure and databanks
, D. Higgins and Taylor, W., Editors. 2000, Oxford
University Press: Oxford New York. p. 15-50.
[29] Rossmann, M.G. and P. Argos,
Exploring structural homology of proteins.
J Mol Biol, 1976.
105
(1): p.
75-95.
[30] Irving, J.A., J.C. Whisstock, and A.M. Lesk,
Protein structural alignments and functional genomics.
Proteins, 2001.
42
(3): p. 378-82.
[31] Willett, P.,
Similarity and clustering in chemical information systems
. 1987, New York: John Wiley &
Sons Inc. 254.
[32] Bajic, V.B.,
Comparing the success of different prediction software in sequence analysis: a review.
Brief Bioinform, 2000.
1
(3): p. 214-28.
[33] Baldi, P., et al.,
Assessing the accuracy of prediction algorithms for classification: an overview.
Bioinformatics, 2000.
16
(5): p. 412-24.
[34] Murvai, J., K. Vlahovicek, and S. Pongor,
A simple probabilistic scoring method for protein domain
identification.
Bioinformatics, 2000.
16
(12): p. 1155-6.
[35] Murvai, J., et al.,
Prediction of protein functional domains from sequences using artificial neural
networks.
Genome Res, 2001.
11
(8): p. 1410-7.
[36] Carugo, O. and S. Pongor,
Protein fold similarity estimated by a probabilistic approach based on
C(alpha)-C(alpha) distance comparison.
J Mol Biol, 2002.
315
(4): p. 887-98.
[37] Evans, M., N. Hastings, and B. Peacock,
Statistical Distributions
. 3nd edition (June 15, 2000) ed.
2000: John Wiley & Sons. 221.
[38] Needleman, S.B. and C.D. Wunsch,
A general method applicable to the search for similarities in the
amino acid sequence of two proteins.
J Mol Biol, 1970.
48
(3): p. 443-53.
[39] Sellers, P.H.,
The theory and computation of evolutionary distances.
Journal of Algorithms, 1980.
1
: p.
359-373.
[40]
Smith, E.E. and D.L. Medin,
Catgories and Concepts
. Cognitive Science Series. 1981, Cambridge,
MA: Harvard University Press. 203.
[41]
Dorogovtsev, S.N. and J.F.F. Mendes,
Evolution of Networks
. 2003, Oxford: Oxford University Press.
264.
